BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525268.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 983,269 number of mapped reads = 899,722 (91.5%) number of supplementary alignments = 3,479 (0.35%) number of secondary alignments = 0 number of mapped bases = 51,982,268 bp number of sequenced bases = 51,965,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,440 duplication rate = 1.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9088 >>>>>>> ACTG content number of A's = 12,481,407 bp (24.02%) number of C's = 9,388,048 bp (18.07%) number of T's = 17,080,000 bp (32.87%) number of G's = 13,014,671 bp (25.04%) number of N's = 1,059 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 261,879 number of insertions = 3,354 mapped reads with insertion percentage = 0.37% number of deletions = 10,704 mapped reads with deletion percentage = 1.18% homopolymer indels = 44.55% >>>>>>> Coverage mean coverageData = 0.0168X std coverageData = 0.1905X There is a 1.57% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5382709 0.02159556906379784 0.32506782555577113 chr2 243199373 4139747 0.01702202990465769 0.2266958404433689 chr3 198022430 3672575 0.018546257613342085 0.14529933570734693 chr4 191154276 2899200 0.015166806940797913 0.13298864305749641 chr5 180915260 2263070 0.012509005597427215 0.11738542654371595 chr6 171115067 3118239 0.018223053379630212 0.1544037208753857 chr7 159138663 3685126 0.02315669825628735 0.3084369847144912 chr8 146364022 3379634 0.02309060624201759 0.2021603112573192 chr9 141213431 1697587 0.012021427338593594 0.14321606600595013 chr10 135534747 3298895 0.024339846961901217 0.2117277648650228 chr11 135006516 2301047 0.017043969936976967 0.1671244766109636 chr12 133851895 2184039 0.016316832869642972 0.1348907458786724 chr13 115169878 1597599 0.01387167398058718 0.1250128012800232 chr14 107349540 1552429 0.014461440635889078 0.12897619307842045 chr15 102531392 1355680 0.01322209689691914 0.12237678308119294 chr16 90354753 1318808 0.014595889604169467 0.13715578300318407 chr17 81195210 873738 0.010760954987369328 0.11150897149241888 chr18 78077248 1086018 0.013909532262202684 0.2651378709848266 chr19 59128983 972274 0.016443272836267113 0.22810172631106018 chr20 63025520 890800 0.014133957165287966 0.12660825821107785 chr21 48129895 709759 0.014746739007014247 0.1306967784404523 chr22 51304566 536169 0.010450707252839834 0.10663881984568938 chrMT 16571 58969 3.5585661698147364 2.5170036687622743 chrX 155270560 2849031 0.018348816414393045 0.15041796573641072 chrY 59373566 159126 0.0026800815703068937 0.07407818676679327